Author, Title, Series? Do you just create a folder for each E Book and label the folder with the books name? I am just trying to get setup...

The crucial thing is to have the right metadata in the files. Calibre does a great job for lrf/epub, while for PDF's you need to use a pdf program that allows you to edit the metadata, using right click - document properties

Once you import then into the Sony software/library, the name/location of the file is irrelevant as long as you do not delete them.

I tend to keep all lrf/pdf's for 700 in one folder, with some in their own folders author based, some not - I made Calibre book directory same so Calibre automatically copies the books there and then I import them to Sony library, and later to the 700, though on the 700 I keep maybe 200 books that I am interested/potentially interested now, while in the Sony library I have quite a few more books

Regarding naming convention - I tend to do Author last name, first name, Title complete, in the metadata, while the files themselves I let Calibre name for the lrf's at least